1qx1: Difference between revisions

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OCA

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-[[Image:1qx1.jpg|left|200px]]<br /><applet load="1qx1" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1qx1, resolution 1.30&Aring;" />
-'''Golgi alpha-mannosidase II D341N mutant complex with 2-F-mannosyl-F'''<br />
-==Overview==
+==Golgi alpha-mannosidase II D341N mutant complex with 2-F-mannosyl-F==
-The family 38 golgi alpha-mannosidase II, thought to cleave mannosidic, bonds through a double displacement mechanism involving a reaction, intermediate, is a clinically important enzyme involved in glycoprotein, processing. The structure of three different covalent glycosyl-enzyme, intermediates have been determined to 1.2-A resolution for the Golgi, alpha-mannosidase II from Drosophila melanogaster by use of fluorinated, sugar analogues, both with the wild-type enzyme and a mutant enzyme in, which the acid/base catalyst has been removed. All these structures reveal, sugar intermediates bound in a distorted 1S5 skew boat conformation. The, similarity of this conformation with that of the substrate in the recently, determined structure of the Michaelis complex of a beta-mannanase (Ducros, V. M. A., Zechel, D. L., Murshudov, G. N., Gilbert, H. J., Szabo, L., Stoll, D., Withers, S. G., and Davies, G. J. (2002) Angew. Chem. Int. Ed., Engl. 41, 2824-2827) suggests that these disparate enzymes have recruited, common stereoelectronic features in evolving their catalytic mechanisms.
+<StructureSection load='1qx1' size='340' side='right'caption='[[1qx1]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1qx1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QX1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QX1 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMF:2-DEOXY-2-FLUOROHEXOPYRANOSYL+FLUORIDE'>FMF</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qx1 OCA], [https://pdbe.org/1qx1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qx1 RCSB], [https://www.ebi.ac.uk/pdbsum/1qx1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qx1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MAN2_DROME MAN2_DROME] Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qx/1qx1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qx1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The family 38 golgi alpha-mannosidase II, thought to cleave mannosidic bonds through a double displacement mechanism involving a reaction intermediate, is a clinically important enzyme involved in glycoprotein processing. The structure of three different covalent glycosyl-enzyme intermediates have been determined to 1.2-A resolution for the Golgi alpha-mannosidase II from Drosophila melanogaster by use of fluorinated sugar analogues, both with the wild-type enzyme and a mutant enzyme in which the acid/base catalyst has been removed. All these structures reveal sugar intermediates bound in a distorted 1S5 skew boat conformation. The similarity of this conformation with that of the substrate in the recently determined structure of the Michaelis complex of a beta-mannanase (Ducros, V. M. A., Zechel, D. L., Murshudov, G. N., Gilbert, H. J., Szabo, L., Stoll, D., Withers, S. G., and Davies, G. J. (2002) Angew. Chem. Int. Ed. Engl. 41, 2824-2827) suggests that these disparate enzymes have recruited common stereoelectronic features in evolving their catalytic mechanisms.
-==About this Structure==
+Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates.,Numao S, Kuntz DA, Withers SG, Rose DR J Biol Chem. 2003 Nov 28;278(48):48074-83. Epub 2003 Sep 5. PMID:12960159<ref>PMID:12960159</ref>
-QX1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] with NAG, ZN, FMF and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,3-1,6-alpha-mannosidase Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.114 3.2.1.114] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QX1 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates., Numao S, Kuntz DA, Withers SG, Rose DR, J Biol Chem. 2003 Nov 28;278(48):48074-83. Epub 2003 Sep 5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12960159 12960159]
+</div>
+<div class="pdbe-citations 1qx1" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Mannosidase 3D structures|Mannosidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Kuntz DA]]
-[[Category: Kuntz, D.A.]]
+[[Category: Numao S]]
-[[Category: Numao, S.]]
+[[Category: Rose DR]]
-[[Category: Rose, D.R.]]
+[[Category: Withers SG]]
-[[Category: Withers, S.G.]]
-[[Category: FMF]]
-[[Category: MPD]]
-[[Category: NAG]]
-[[Category: ZN]]
-[[Category: covalent catalytic intermediate]]
-[[Category: glycosyl hydrolase family 38]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:04:57 2007''